The DeepChek® Assay Whole Genome SARS-CoV-2 Genotyping is a RT-PCR Assay (nucleic acid technique (NAT)) followed by Next Generation Sequencing (NGS) intended to aid clinical applications and for use on previously diagnosed COVID-19 patients.
Intended Use (CE-IVD) — REF 159A48
The DeepChek® Assay Whole Genome SARS-CoV-2 Genotyping V1 is intended to be used for amplifying whole-genome of severe acute respiratory syndrome-associated coronavirus 2 (SARS-CoV-2) in upper respiratory specimens (such as nasal, mid-turbinate, nasopharyngeal, and oropharyngeal swab specimens, and nasopharyngeal wash/aspirate or nasal aspirate specimens) from individuals already tested positive to SARS-CoV-2.
The DeepChek® Assay Whole Genome SARS-CoV-2 Genotyping V1 aims to identify SARS-CoV-2 infection by a variant (or lineage) which might aid in clinical applications.
This nucleic amplification test is indicated for use on previously diagnosed COVID-19 patients ONLY. This test is NOT intended to be used as a screening or confirmation test for the detection, confirmation or quantification in upper respiratory specimens of SARS-CoV-2.
Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) and Next Generation Sequencing.
The Assay targets and amplify the whole genome (>99%) of SARS-CoV-2 virus, including regions that harbor mutations of interest described as sufficient in databases like Pangolin and Nextclade, including: UK, Indian, South African, Brazilian variants of concern (VOC).
The DeepChek® Assay Whole Genome SARS-CoV-2 Genotyping V1 is intended for use by qualified clinical laboratory personnel specifically instructed and trained in the techniques of PCR, next generation sequencing workflow and in vitro diagnostic procedures. The current laboratory biosafety guidance for the 2019 novel coronavirus (SARS-CoV-2) shall be followed.
Post PCR – Complementary information
Next Generation Sequencing
The main volume of the product output is then used for next generation sequencing (NGS). The NGS workflow can be
different as the NGS technics and NGS analyzers vary. NGS sequencing instruments are general laboratory use devices.
Sequencing and library preparations reagents are general laboratory use products.
While the validation studies, we used the Illumina iSeq 100 Sequencing System (#20021532) and the following combination
of reagents: ABL DeepChek® NGS Library preparation (catalog #116AX, 24 or 48 or 96 tests), ABL DeepChek® Assay Adapters (catalog #124AX, 1-24, 1-48 or 1-96) and Illumina iSeq 100 Reagent (catalog # 20021533, 300 cycles).
Note: The external clinical study was conducted with Illumina MiSeq NGS analyzer and related MiSeq Reagent Kit, v2 (catalog # MS-102-2003, 500 cycles) with no need to perform the fragmentation step with the ABL DeepChek® NGS Library preparation (catalog #116AX, 24 or 48 or 96 tests).
Downstream NGS Analysis Software
The sequencing raw data are then uploaded in a specific downstream software tailored for SARS-CoV-2 whole genome analysis and interpretation. This software is a standalone medical device. The software itself can be CE-IVD marked and shall rely on recognized and updated public sources about SARS-CoV-2 circulating strains and SARS-CoV-2 lineage definitions and latest knowledge about the clinical impact of genomic variations.
For the validation studies and the external clinical validation study, the next generation sequencing raw data , outputs from Illumina iSeq100 and MiSeq NGS analyzers, were uploaded in a specific downstream software tailored for SARS-CoV-2 analysis which is a standalone medical device: ABL DeepChek® -CoV-2 software (RUO) (licence and module (catalog #S-12-023 (CVL) and #S-12-023 (CVM)).
The DeepChek® Whole Genome SARS-CoV-2 Genotyping Assay can be part of a laboratory validated environment for an end-to-end solution including laboratory automation (liquid handling robot) and laboratory information system integration with the laboratory information system (LIS).
More information on the DeepCheck® SARS CoV-2 Whole Genome – Click here
CE marking only valid for EEA and territories recognizing it – Otherwise it is for RUO application.
Characteristics and performances
RT-PCR Assay followed by NGS (Next Generation Sequencing)
>99% genome covered by Multiplex targeting SARS CoV-2 whole genome
RNA extraction and purification of clinical specimen
MagNa Pure 24 instrument (Roche;
Catalog #07290519001B) with the MagNA Pure 24 Total NA Isolation Kit (Roche, Catalog #07658036001)
Note: Any laboratory validated instrument for RNA extraction and purification using magnetic-bead technology shall work with the test (i.e. bioMérieux EMAG®, Perkin Elmer ChemagicTM 360, ThermoFisher Scientific MagMAX Viral/Pathogen Nucleic Acid Isolation Kit, Qiagen QIAamp Viral RNA Mini Kit, Biopur® Mini Spin Plus Kit and Magtivio MagSi-NA Pathogens).
ThermoFisher Scientific ProFlex™ PCR System (model 3 x 32-well (Catalog #4484073) or 96-well (Catalog
#4484075) and associated specific material.
Note: Any laboratory validated thermal cycler with enough ramp rate of ≥ 1°C/s shall be sufficient.
Validated with NGS platforms
Note: Any laboratory validated instrument for NGS shall work with the test
Format / Models
- 48 tests/kit (159A48)
- CoV Reaction Solution (Master Mix 2X, RT Mix)
- Whole Genome Primers
- Positive Control
- Negative Control
- Molecular Grade Water
Estimated turnaround time
[48 - 72 h]
Limit of Detection (LoD)
The concentration level for the DeepChek Assay Whole Genome SARS-CoV-2 Genotyping V1 with observed rates greater than or equal to 95% was 0.000115 TCID50/mL for SARS-CoV-2 with the ProFlex™ 3 x 32-well PCR System (Catalog #4484073).
Among the tested samples with specific clades (UK or SA): 100% were adequately amplified, sequenced and characterized, either as B.1.1.7 or B.1.351, by the DeepChek CoV2 software following the DeepChek Assay Whole Genome SARS-CoV-2 Genotyping V1.
Inclusivity (analytical reactivity)
The DeepChek Assay Whole Genome SARS-CoV-2 Genotyping V1 has excellent coverage of all reported circulating SARS-CoV-2 strains in the Inclusivity dataset (121 358 unique sequences after removal of low identity and low coverage alignments)
Cross-reactivity (In Silico )
All pathogens were determined to have no cross-reactivity with the primers pairs used for the the DeepChek Assay Whole Genome SARS-CoV-2 Genotyping V1
Cross-reactivity (Wet testing)
For cross-reactivity wet testing, the DeepChek Assay Whole Genome SARS-CoV-2 Genotyping V1 did not react for most of the tested microorganisms that are commonly found in upper respiratory specimens and tested at the indicated concentration
The positive (PPA) and negative (NPA) percent agreements between the DeepChek Assay Whole Genome SARS-CoV-2
Genotyping V1 and the CE-IVD comparator assay are:
PPA = 30/30 = 100% (95% C.I. = 88.65% - 100%)
NPA = 30/30 = 100% (95% C.I. = 88.65% - 100%)
The agreement between the two tests (93.5%) was perfect (Cohen’s kappa = 0.87) for variants detection
100% results accuracy both for SARS-CoV-2 clade identification and defining mutations used for clade identification (Nexstrain SARS-CoV-2)
External clinical validation
Among the 255 successful samples, the SARS-CoV-2 clades identified as variants of concern (VOC) (n=102, 40.0%) were identified with 29.4% (20H/501Y.V2)(SA), 5.9% (20J/501Y.V3)(BR) and 4.7% (20I/501Y.V1) (UK1). Among the other SARSCoV-2 clades identified, the DeepChek Assay Whole Genome SARS-CoV-2 Genotyping V1 detected one of the first cases in France for the Indian double mutant (20A/484Q (B.1.617)). A subset of 10 samples (extracted RNA) were also sent for results validation by the French SARS-CoV-2 CNR (Centre National de Référence des virus respiratoires): 100% results accuracy was reached with the CNR whole genome sequencing workflow and the DeepChek Assay Whole Genome SARSCoV-2 Genotyping V1
DeepChek Assay Whole Genome SARS-CoV-2 Genotyping V1 (48 tests) (CE-IVD)
EC Declaration of Conformity